Japanese tried to introduce radically new designs, and build radically different fighters for different purposes (they wanted specialized interceptors, that had nothing in common with general purpose fighters, and so on).
With the exception of the Shinden and a very few others, most Japanese fighter designs were not radical in nature. They were not radical engineering departures from their previous fighters. Design to meet different missions, true. But the engineering contained within them was conventional. Their use of substitiute materials in many cases was innovative but introduced an entire new set of growing pains.
Late war Japanese aircraft such as the George and the Frank had the potential to go 1 on 1 vs most allied aircraft but engine reliability issues severely limited their performance. In many cases, their engines were only able to develop less than 75% of their standard horsepower. Reduced oil pressure caused by excessive bearing tolerances and poorly performing superchargers were the main culprits. But when they worked, they could hold their own against allied opposition... assuming of course, a good pilot could be found to fly it.
And as you state, one of their biggest problems was the lack of coordination between the services. Each was highly secretive and took extreme measures to ensure the other service was kept in the dark. Yoshimura, in his book "Zero Fighter", tells the story of the A6M and the extreme security surrounding its development. Navy officials forbid Mitsubishi workers who worked on Army projects from even entering the hangar where the A6M prototype was developed.
Chez